No, move the Be Quiet to the intake and everything should be fine.
TC14PE is a classic, Dark Rock Pro 3 or 4. Cheaper as in one of the cheaper dual towers, not cheaper than the NH-U12S, but in the same ballpark as the NH-U14S, unlike e.g. the NH-D15.
Le Grand Macho RT is also an option. Single tower, but with the volume of a dual tower. Obviously quieter than a dual tower with twice the fans and still pretty good cooling. At the same loudness actually a bit cooler than the NH-U14S, it just tops out at 1300 rpm instead of 1500 rpm like most others so at 100% the U14S gets marginally lower temps.
The Z370-A Pro doesn't actually use the first PCIe slot allowed in the ATX spec. They've put an M.2 slot there and the 2nd out of the 7 ATX PCIe slot positions is where the actual first slot is on the mobo. That means it'll be spaced out by one slot no matter what. Never put the GPU in anything but the top x16 slot, all others are significantly slower. I'm assuming that means the RAM is in slots 2 and 4 counting from the CPU, as it should be. At most the NH-U14S should overhand the first slot and even then it's tall enough to fit 32mm RAM beneath it. So any RAM will fit and if you need all 4 slots just don't buy anything with ridiculous extra high heat spreaders.